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Crystal structure of the 2-keto-3-deoxy-6-phosphogluconate aldolase of zymomonas mobilis ZM4
Analyse Crystal structure of the 2-keto-3-deoxy-6-phosphogluconate aldolase of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XSE
- Type
- protein
- Length
- 622 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- KHG/KDPG aldolase
- EC
- 4.1.2.14
- UniProt
- Q00384
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | KHG/KDPG aldolase (EC 4.1.2.14) | protein | 208 | 41% helix, 17% strand | Q00384 |
| B | KHG/KDPG aldolase (EC 4.1.2.14) | protein | 207 | 42% helix, 17% strand | Q00384 |
| C | KHG/KDPG aldolase (EC 4.1.2.14) | protein | 207 | 42% helix, 18% strand | Q00384 |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 738 | 0.78 | 0.82 | 124 | empty |
| 2 | 354 | 0.67 | 0.81 | 33 | empty |
| 3 | 83 | 0.35 | 0.75 | 20 | empty |
| 4 | 75 | 0.34 | 0.75 | 19 | empty |
| 5 | 63 | 0.30 | 0.75 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–B · 617 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 608 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 571 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5XSE · Crystal structure of the 2-keto-3-deoxy-6-phosphogluconate aldolase of Zymomonas mobilis… · the same entry in another collection · chain A against A, TM-score 1.00
- Q00384 · AlphaFold monomer V2.0 prediction for KHG/KDPG aldolase (Q00384) · a predicted model of the same protein · chain B against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q00384
- Elsewhere: RCSB PDB 5XSE · PDBe 5XSE · UniProt Q00384
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